1S20 | pdb_00001s20

A novel NAD binding protein revealed by the crystal structure of E. Coli 2,3-diketogulonate reductase (YiaK) NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER82

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H	d1s20h1	Alpha and beta proteins (a/b)	L-sulfolactate dehydrogenase-like	L-sulfolactate dehydrogenase-like	L-sulfolactate dehydrogenase-like	2,3-diketogulonate oxidoreductase (YiaK)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H	d1s20h2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G	d1s20g1	Alpha and beta proteins (a/b)	L-sulfolactate dehydrogenase-like	L-sulfolactate dehydrogenase-like	L-sulfolactate dehydrogenase-like	2,3-diketogulonate oxidoreductase (YiaK)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G	d1s20g2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d1s20f1	Alpha and beta proteins (a/b)	L-sulfolactate dehydrogenase-like	L-sulfolactate dehydrogenase-like	L-sulfolactate dehydrogenase-like	2,3-diketogulonate oxidoreductase (YiaK)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d1s20f2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d1s20e1	Alpha and beta proteins (a/b)	L-sulfolactate dehydrogenase-like	L-sulfolactate dehydrogenase-like	L-sulfolactate dehydrogenase-like	2,3-diketogulonate oxidoreductase (YiaK)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d1s20e2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1s20d1	Alpha and beta proteins (a/b)	L-sulfolactate dehydrogenase-like	L-sulfolactate dehydrogenase-like	L-sulfolactate dehydrogenase-like	2,3-diketogulonate oxidoreductase (YiaK)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1s20d2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1s20c1	Alpha and beta proteins (a/b)	L-sulfolactate dehydrogenase-like	L-sulfolactate dehydrogenase-like	L-sulfolactate dehydrogenase-like	2,3-diketogulonate oxidoreductase (YiaK)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1s20c2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1s20b1	Alpha and beta proteins (a/b)	L-sulfolactate dehydrogenase-like	L-sulfolactate dehydrogenase-like	L-sulfolactate dehydrogenase-like	2,3-diketogulonate oxidoreductase (YiaK)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1s20b2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1s20a1	Alpha and beta proteins (a/b)	L-sulfolactate dehydrogenase-like	L-sulfolactate dehydrogenase-like	L-sulfolactate dehydrogenase-like	2,3-diketogulonate oxidoreductase (YiaK)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1s20a2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	L-sulfolactate dehydrogenase-like	8033716	3000527	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	L-sulfolactate dehydrogenase-like	8033716	3000527	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	L-sulfolactate dehydrogenase-like	8033716	3000527	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	L-sulfolactate dehydrogenase-like	8033716	3000527	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	L-sulfolactate dehydrogenase-like	8033716	3000527	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	L-sulfolactate dehydrogenase-like	8033716	3000527	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	L-sulfolactate dehydrogenase-like	8033716	3000527	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	L-sulfolactate dehydrogenase-like	8033716	3000527	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	Amidase_2	e1s20H1	A: a/b three-layered sandwiches	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: Amidase_2	ECOD (v294.1)
G	Amidase_2	e1s20G1	A: a/b three-layered sandwiches	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: Amidase_2	ECOD (v294.1)
F	Amidase_2	e1s20F1	A: a/b three-layered sandwiches	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: Amidase_2	ECOD (v294.1)
E	Amidase_2	e1s20E1	A: a/b three-layered sandwiches	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: Amidase_2	ECOD (v294.1)
D	Amidase_2	e1s20D1	A: a/b three-layered sandwiches	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: Amidase_2	ECOD (v294.1)
C	Amidase_2	e1s20C1	A: a/b three-layered sandwiches	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: Amidase_2	ECOD (v294.1)
B	Amidase_2	e1s20B1	A: a/b three-layered sandwiches	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: Amidase_2	ECOD (v294.1)
A	Amidase_2	e1s20A1	A: a/b three-layered sandwiches	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: Amidase_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	1.10.1530.10	Mainly Alpha	Orthogonal Bundle	Hypothetical Oxidoreductase Yiak	Chain: A, domain 1	CATH (4.3.0)
H	3.30.1370.60	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
H	3.30.60.50	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
G	1.10.1530.10	Mainly Alpha	Orthogonal Bundle	Hypothetical Oxidoreductase Yiak	Chain: A, domain 1	CATH (4.3.0)
G	3.30.1370.60	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
G	3.30.60.50	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
F	1.10.1530.10	Mainly Alpha	Orthogonal Bundle	Hypothetical Oxidoreductase Yiak	Chain: A, domain 1	CATH (4.3.0)
F	3.30.1370.60	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
F	3.30.60.50	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
E	1.10.1530.10	Mainly Alpha	Orthogonal Bundle	Hypothetical Oxidoreductase Yiak	Chain: A, domain 1	CATH (4.3.0)
E	3.30.1370.60	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
E	3.30.60.50	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
D	1.10.1530.10	Mainly Alpha	Orthogonal Bundle	Hypothetical Oxidoreductase Yiak	Chain: A, domain 1	CATH (4.3.0)
D	3.30.1370.60	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
D	3.30.60.50	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
C	1.10.1530.10	Mainly Alpha	Orthogonal Bundle	Hypothetical Oxidoreductase Yiak	Chain: A, domain 1	CATH (4.3.0)
C	3.30.1370.60	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
C	3.30.60.50	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
B	1.10.1530.10	Mainly Alpha	Orthogonal Bundle	Hypothetical Oxidoreductase Yiak	Chain: A, domain 1	CATH (4.3.0)
B	3.30.1370.60	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
B	3.30.60.50	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
A	1.10.1530.10	Mainly Alpha	Orthogonal Bundle	Hypothetical Oxidoreductase Yiak	Chain: A, domain 1	CATH (4.3.0)
A	3.30.1370.60	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
A	3.30.60.50	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF02615	Malate/L-lactate dehydrogenase (Ldh_2)	Malate/L-lactate dehydrogenase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Hypothetical oxidoreductase yiaK	NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors catalytic activity 3-dehydro-L-gulonate 2-dehydrogenase activity	-	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR023689	2,3-diketo-L-gulonate reductase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR043143	Malate/L-sulfolactate/L-lactate dehydrogenase-like, NADPH binding domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR043144	Malate/L-sulfolactate/L-lactate dehydrogenase-like, alpha-helical domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR003767	Malate/L-lactate dehydrogenase-like	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036111	Malate/L-sulfolactate/L-lactate dehydrogenase-like superfamily	Homologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	3-dehydro-L-gulonate 2-dehydrogenase M-CSA #765	2,3-Diketo-L-gulonate reductase (yiaK) is from Escherichia coli. It is the first gene in a nine-gene sequence operon, which is believed to be required for the utilisation of rare sugars for growth. YiaK catalyses the reduction of 2,3-diketo-L-gulonate (DKG) in the presence of NADH to give 3-keto-L-gulonate.	Defined by 1 residue: HIS:A-44 \| Explore in 3D: M-CSA Motif Definition At least 2 residues must be present to support Structure Motif searching. EC: 1.1.1 (PDB Primary Data) EC: 1.1.1.130 (UniProt)

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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